Introduction
          Overview
          Overview of Rule-Based Features
          General Navigation and Window Setup
          Top Menu
          File
               File -> New
               File -> Open
               File -> Save As
               File -> Revert To Saved
               File -> Permissions
               File -> Model Annotation
               File -> Edit Annotation
               File -> Field Data
               File -> Import
               File -> Import (BNGL files)
               File -> Export
          Server
               User Login
               Change User
               Update Registration Information
               New User Registration
          Window
          Tools
               Launch BioNetGen
                    BioNetGen Rules editor tab
                    BioNetGen Messages tab
                    BioNetGen Output tab
                    BioNetGen Help tab
               Launch VFRAP
               VisIt Visualization Tool
               Transform to Stochastic Capable
          Help
     Overview of Rule-Based Features
          Introduction to Rule-Based Modeling
          How to create a rule-based model
          How to simulate a rule-based model
          Network-Free Application
     Physiology Overview
          Reactions Diagram
          Reactions Table
               Reactions Properties Pane
               Membrane Flux Properties Pane
               Reactions Rules Editor Pane
               Reactions Rules Kinetics Pane
               Pathway Links
          Physiology Structures Tabular View
               Structure Properties Pane
          Species Table
               Species Properties Pane
               Pathway Links
          Molecules Table
               Molecules Properties Pane
          Observables Table
               Observable Properties Pane
     Applications Overview
          Geometry Overview
               Creating analytic geometries in VCell
               Creating image-based geometries in VCell
               Creating Geometries from STL files
               Geometry Structure Mapping
                    Structure Mapping for spatial geometries
                    Structure Mapping for non-spatial geometries
          Specifications Overview
               Species Specifications
                    Field Data - Incorporating experimental data in simulations
               Reactions Specifications
               Network Specifications
               Network-Free Specifications
          Protocols Overview
               Events
               Electrical Mapping
               Microscope Measurements
          Simulations Overview
               Simulations
               Simulations Editor
               NFSim Simulations Editor
               Output Functions
               Generated Math
               Numerical Solvers
               Simulation Results
                    Spatial Simulation Results Overview
                         Spatial Simulation Results Slice/Surface View
                         Region of Interest Tools
                         Membrane Surface Viewer
                         Statistics
                         Simulation Results Viewer Plots
                         Post Processing Statistics Data
                         Post Processing Image Data
                         Exporting Spatial Simulation Results
                         Specific Format Settings
                    Compartment Simulation Results Viewer
                         Compartmental Simulation Results Plot Settings
                         Stochastic Simulation Results Histograms
          Parameter Estimation Overview
               COPASI Optimization Methods Overview
               How to use parameter estimation in Virtual Cell
     Parameters and Functions Overview
          Parameters and Functions
          Predefined Constants and Math Functions
          VCell Model Units
     Biological Pathways Overview
          Pathway Commons Database
          Pathway Preview
          Pathway Diagram View
          Pathway Objects Table View
          BioPAX Summary
          BioPAX Tree
          Pathways Object Properties Pane
          Entities Management Toolbar
     Database Sources
          VCell Database
          BioModels Database
          Pathway Commons Database
          SABIO-RK - Biochemical Reaction Kinetics Database
     Properties Panes
          Application Properties Pane
          Database Info Properties Pane
          Membrane Flux Properties Pane
          Molecules Properties Pane
          Observable Properties Pane
          Parameter Properties Pane
          Pathways Object Properties Pane
          Problems Tab
          Reactions Properties Pane
          Reactions Rules Editor Pane
          Reactions Rules Kinetics Pane
          Species Properties Pane
          Stoichiometry Tab
          Structure Properties Pane
     Appendix
          Error List
          Warnings